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The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with 2-fluoroglucopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native Os4BGlu12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 288.15 19% PEG 2000, 0.1M Tris HCl, 0.16M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.15K
Crystal Properties Matthews coefficient Solvent content 2.62 52.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.046 α = 90 b = 114.046 β = 90 c = 184.149 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2009-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 30 99.6 0.104 3.4 6.2 48324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 99.6 0.53 3.4 6.2 48324
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT native Os4BGlu12 2.4 25.86 45810 2441 99.83 0.19774 0.19579 0.1942 0.23432 0.2331 RANDOM 28.611
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.46 0.46 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.436 r_dihedral_angle_4_deg 19.965 r_dihedral_angle_3_deg 15.197 r_dihedral_angle_1_deg 5.547 r_scangle_it 1.136 r_angle_refined_deg 1.015 r_scbond_it 0.683 r_mcangle_it 0.574 r_nbtor_refined 0.305 r_mcbond_it 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.436 r_dihedral_angle_4_deg 19.965 r_dihedral_angle_3_deg 15.197 r_dihedral_angle_1_deg 5.547 r_scangle_it 1.136 r_angle_refined_deg 1.015 r_scbond_it 0.683 r_mcangle_it 0.574 r_nbtor_refined 0.305 r_mcbond_it 0.305 r_nbd_refined 0.181 r_symmetry_vdw_refined 0.179 r_xyhbond_nbd_refined 0.115 r_symmetry_hbond_refined 0.101 r_metal_ion_refined 0.093 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7722 Nucleic Acid Atoms Solvent Atoms 511 Heterogen Atoms 59
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling